Molecular detection and Phylogenetic Characterisation of Salivirus genotype A2 in Wastewater from Zambia’s Copperbelt and Eastern Provinces

Abstract

Salivirus (SalV), a member of the Picornaviridae family, is a novel virus associated with acute gastroenteritis. In Zambia, its prevalence and genetic diversity remain uncharacterized. We analyzed 87 raw wastewater samples from 12 sites in the Copperbelt and Eastern Provinces using next-generation sequencing. SalV was detected in 43.7% of samples, with 42.1% yielding full-length open reading frames. Phylogenetic analysis revealed that all sequences belonged to genotype A2 and were closely related to human-derived strains. SalV sequences from both provinces belonged to genotype A2 and were closely related to previous strains detected in humans. To our knowledge, this is the first report of Salivirus genotype A2 detection in raw wastewater in Zambia, highlighting the need for environmental surveillance to monitor enteric pathogens.